Sodium in PDB 1s5e: Cholera Holotoxin, Crystal Form 1

All present enzymatic activity of Cholera Holotoxin, Crystal Form 1:
2.4.2.36;

The structure of Cholera Holotoxin, Crystal Form 1, PDB code: 1s5e was solved by C.J.O'neal, E.I.Amaya, M.G.Jobling, R.K.Holmes, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.82 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.931, 108.230, 122.976, 90.00, 95.89, 90.00
R / Rfree (%)	16.7 / 20.5

The binding sites of Sodium atom in the Cholera Holotoxin, Crystal Form 1 (pdb code 1s5e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cholera Holotoxin, Crystal Form 1, PDB code: 1s5e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cholera Holotoxin, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cholera Holotoxin, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na241 b:23.7 occ:1.00 O A:TYR150 2.3 20.3 1.0 O A:LEU153 2.3 21.4 1.0 O A:HOH262 2.4 20.8 1.0 OG1 A:THR90 2.5 19.7 1.0 O A:ASN1 2.5 10.4 1.0 O A:THR90 2.5 23.9 1.0 C A:LEU153 3.3 22.2 1.0 C A:THR90 3.4 21.9 1.0 C A:TYR150 3.5 21.3 1.0 N A:THR90 3.6 21.6 1.0 CB A:THR90 3.6 21.8 1.0 CA A:THR90 3.7 22.2 1.0 C A:ASN1 3.7 12.5 1.0 N A:LEU153 4.1 22.8 1.0 CA A:SER151 4.1 23.6 1.0 CA A:LEU153 4.1 21.9 1.0 N A:ASN1 4.2 11.4 1.0 N A:SER151 4.2 22.3 1.0 N A:ASP154 4.2 22.9 1.0 CB A:LEU153 4.3 22.8 1.0 CA A:ASP154 4.4 24.2 1.0 CA A:TYR150 4.5 20.6 1.0 C A:SER151 4.5 24.3 1.0 O A:ASP3 4.5 10.7 1.0 O A:HOH252 4.5 30.9 1.0 N A:ALA91 4.5 22.7 1.0 C A:ALA89 4.6 21.8 1.0 CA A:ASN1 4.6 13.0 1.0 N A:ASP2 4.7 13.0 1.0 CA A:ASP2 4.7 14.3 1.0 CB A:TYR150 4.7 19.9 1.0 CB A:ALA89 4.7 22.3 1.0 CG2 A:THR90 4.8 23.1 1.0 O A:SER151 4.8 24.2 1.0 OD1 A:ASN1 4.8 15.3 1.0 N A:ASP3 4.8 13.5 1.0 N A:ASN152 4.9 25.1 1.0 OD1 A:ASP154 4.9 28.5 1.0 C A:ASP2 5.0 14.6 1.0 CA A:ALA89 5.0 21.4 1.0

Sodium binding site 2 out of 2 in the Cholera Holotoxin, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cholera Holotoxin, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na241 b:23.3 occ:1.00 O B:HOH267 2.2 22.2 1.0 O B:LEU153 2.4 8.5 1.0 O B:TYR150 2.4 6.0 1.0 OG1 B:THR90 2.5 8.9 1.0 O B:THR90 2.5 8.8 1.0 O B:ASN1 2.5 7.7 1.0 C B:THR90 3.4 8.1 1.0 C B:LEU153 3.4 9.3 1.0 C B:TYR150 3.5 7.0 1.0 N B:THR90 3.5 6.8 1.0 CB B:THR90 3.6 8.7 1.0 CA B:THR90 3.7 7.9 1.0 C B:ASN1 3.8 10.8 1.0 N B:LEU153 4.1 8.7 1.0 CA B:SER151 4.2 7.2 1.0 CA B:LEU153 4.2 8.9 1.0 O B:HOH262 4.3 30.1 1.0 N B:SER151 4.3 6.4 1.0 N B:ASN1 4.3 9.0 1.0 N B:ASP154 4.3 9.6 1.0 O B:ASP3 4.3 9.4 1.0 O B:HOH257 4.4 28.1 1.0 CB B:LEU153 4.4 8.2 1.0 CA B:ASP154 4.5 10.6 1.0 CA B:TYR150 4.5 8.2 1.0 C B:SER151 4.5 9.7 1.0 C B:ALA89 4.5 7.6 1.0 CB B:ALA89 4.5 8.6 1.0 N B:ALA91 4.6 8.6 1.0 CA B:ASP2 4.7 12.1 1.0 N B:ASP2 4.7 10.8 1.0 CA B:ASN1 4.7 10.3 1.0 CG2 B:THR90 4.7 8.6 1.0 CB B:TYR150 4.7 8.2 1.0 N B:ASP3 4.8 10.5 1.0 O B:SER151 4.8 8.5 1.0 OD1 B:ASN1 4.8 14.3 1.0 OD1 B:ASP154 4.9 14.6 1.0 CA B:ALA89 4.9 7.6 1.0 C B:ASP2 4.9 11.7 1.0

C.J.O'neal, E.I.Amaya, M.G.Jobling, R.K.Holmes, W.G.Hol. Crystal Structures of An Intrinsically Active Cholera Toxin Mutant Yield Insight Into the Toxin Activation Mechanism Biochemistry V. 43 3772 2004.
ISSN: ISSN 0006-2960
PubMed: 15049684
DOI: 10.1021/BI0360152